# Build everything necessary to compile the wiki.
-SUBDIRS = posts/Abax posts/drexel-thesis posts/Hooke posts/problempack \
+SUBDIRS = posts/drexel-thesis posts/Hooke posts/problempack \
posts/rel-vcs posts/sawsim posts/Thesis posts/yacc2dot posts/Xmodmap \
posts/XSLT/chapter posts/XSLT/code
TARGETS = all clean
manner, so users don't need to worry about sharing resources fairly or
[[ssh]]ing into compute nodes to start their jobs. Users submit jobs
to the queue using `qsub`. I've compiled my own [[brief
-intro|pbs_queues.pdf]] to `qsub`, and there are lots more floating
-about the internet.
+intro|pbs_queues]] to `qsub`, and there are lots more floating about
+the internet.
While PBS queues are great for distributing embarassingly parallel
jobs across the cluster, your application may need processes running
+++ /dev/null
-all: pbs_queues.pdf
-
-clean:
- rm -rf pbs_queues.pdf
- $(MAKE) -C pbs_queues latex-clean pdf-clean # no Torque/Maui on webserver
-
-pbs_queues.pdf: pbs_queues/main.pdf
- cp $< $@
-
-.PHONY: pbs_queues/main.pdf
-pbs_queues/main.pdf:
- $(MAKE) -C pbs_queues main.pdf
--- /dev/null
+[[!meta title="Batch Queue Job Control"]]
+
+<a name="qsub" />
+
+Submitting jobs
+===============
+
+You can submit jobs to the batch queue for later proccessing with
+`qsub`. Batch queueing can get pretty fancy, so `qsub` comes with
+lots of options (see `man qsub`). For the most part, you can trust
+your sysadmin to have set up some good defaults, and not worry about
+setting any options explicitly. As you get used to the batch queue
+system, you'll want tighter control of how your jobs execute by
+invoking more sophisticated options yourself, but don't let that scare
+you off at the beginning. They are, after all, only *options*. This
+paper will give you a good start on the options I find myself using
+most often.
+
+Simple submission
+-----------------
+
+The simplest example of a job submission is:
+
+ $ echo "sleep 30 && echo 'Running a job...'" | qsub
+ 2705.n0.physics.drexel.edu
+
+Which submits a job executing `sleep 30 && echo 'Running a job...'`
+to the queue. The job gets an identifying ID in the queue, which
+`qsub` prints to `stdout`.
+
+You can check the status of your job in the queue with `qstat`.
+
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2705.n0 STDIN sysadmin 0 Q batch
+
+There is more information on `qstat` in the [qstat section][sec.qstat].
+
+If your job is too complicated to fit on a single line, you can save
+it in a script:
+
+ #!/bin/bash
+ # file: echo_script.sh
+ sleep 30
+ echo "a really,"
+ echo "really,"
+ echo "complicated"
+ echo "script"
+
+and submit the script:
+
+ $ qsub echo_script.sh
+ 2706.n0.physics.drexel.edu
+
+All the arguments discussed in later sections for the command line
+should have comment-style analogs that you can enter in your script if
+you use the script-submission approach with `qsub`.
+
+Note that you *cannot* run executibles directly with `qsub`. For
+example
+
+ $ cat script.py
+ #!/usr/bin/python
+ print("hello world!")
+ $ qsub python script.py
+
+will fail because `python` is an executible.
+Either use
+
+ $ echo python script.py | qsub
+
+wrap your [[Python]] script in a [[Bash]] script
+
+ $ cat wrapper.sh
+ #!/bin/bash
+ python script.py
+ $ qsub wrapper.sh
+
+or run your Python script directly (relying on the sha-bang)
+
+ $ qsub script.py
+
+IO: Job names and working directories
+-------------------------------------
+
+You will often be interested in the `stdout` and `stderr` output from
+your jobs. The batch queue system saves this information for you (to
+the directory from which you called `qsub`) in two files
+`<jobname>.o<jobID-number>` and `<jobname>.e<jobID-number>`. Job IDs
+we have seen before, they're just the numeric part of `qsub` output
+(or the first field in the `qstat` output). Job IDs are assigned by
+the batch queue server, and are unique to each job. Job names are
+assigned by the job submitter (that's you) and need not be unique.
+They give you a method for keeping track of what job is doing what
+task, since you have no control over the job ID. The combined
+`<jobname>.<jobID-number>` pair is both unique (for the server) and
+recognizable (for the user), which is why it's used to label the
+output data from a given job. You control the job name by passing the
+`-N <jobname>` argument to `qsub`.
+
+ $ echo "sleep 30 && echo 'Running a job...'" | qsub -N myjob
+ 2707.n0.physics.drexel.edu
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2707.n0 myjob sysadmin 0 Q batch
+
+Perhaps you are fine with `stdin` and `stdout`, but the default naming
+scheme, even with the job name flexibility, is too restrictive. No
+worries, `qsub` lets you specify exactly which files you'd like to use
+with the unsurprisingly named `-o` and `-e` options.
+
+ $ echo "echo 'ABC' && echo 'DEF' > /dev/stderr" | qsub -o my_out -e my_err
+ 2708.n0.physics.drexel.edu
+ … time passes …
+ $ cat my_out
+ ABC
+ $ cat my_err
+ DEF
+
+A time will come when you are no longer satified with `stdin` and
+`stdout` and you want to open your own files or worse, run a program!
+Because no sane person uses absolute paths all the time, we need to
+know what directory we're in so we can construct our relative paths.
+You might expect that your job will execute from the same directory
+that you called qsub from, but that is not the case. I think the
+reason is that that directory is not garaunteed to exist on the host
+that eventually runs your program. In any case, your job will begin
+executing in your home directory. Writing relative paths from your
+home directory is about as annoying as writing absolute paths, so
+`qsub` gives your script a nifty environment variable `PBS_O_WORKDIR`,
+which is set to the directory you called `qsub` from. Since *you*
+know that this directory exists on the hosts (since the home
+directories are NFS mounted on all of our cluster nodes), you can move
+to that directory yourself, using something like
+
+ $ echo 'pwd && cd $PBS_O_WORKDIR && pwd' | qsub
+ 2709.n0.physics.drexel.edu
+ … time passes …
+ $ cat STDIN.o2709
+ /home/sysadmin
+ /home/sysadmin/howto/cluster/pbs_queues
+
+Note that if we had enclosed the echo argument in double quotes (`"`),
+we would have to escape the `$` symbol in our `echo` argument so that
+it survives the shell expansion and makes it safely into `qsub`'s
+input.
+
+Long jobs
+---------
+
+If you have jobs that may take longer than the default wall time
+(currently 1 hour), you will need to tell the job manager. Walltimes
+may seem annoying, since you don't really know how long a job will run
+for, but they protect the cluster from people running broken programs
+that waste nodes looping around forever without accomplishing
+anything. Therefor, your walltime doesn't have to be exactly, or even
+close to, your actual job execution time. Before submitting millions
+of long jobs, it is a good idea to submit a timing job to see how long
+your jobs should run for. Then set the walltime a factor of 10 or so
+higher. For example
+
+ $ echo "time (sleep 30 && echo 'Running a job...')" | qsub -j oe
+ 2710.n0.physics.drexel.edu
+ … time passes …
+ $ cat STDIN.o2710
+ Running a job...
+
+ real 0m30.013s
+ user 0m0.000s
+ sys 0m0.000s
+ $ echo "sleep 30 && echo 'Running a job...'" | qsub -l walltime=15:00
+ 2711.n0.physics.drexel.edu
+ $ qstat -f | grep '[.]walltime'
+
+You can set walltimes in `[[H:]M:]S` format, where the number of
+hours, minutes, and seconds are positive integers. I passed the `-j
+oe` combines both `sdtout` and `stdin` streams on `stdin` because
+`time` prints to `stderr`. Walltimes are only accurate on the order
+of minutes and above, but you probably shouldn't be batch queueing
+jobs that take less time anyway.
+
+Job dependencies
+----------------
+
+You will often find yourself in a situation where the execution of one
+job depends on the output of another job. For example, `jobA` and
+`jobB` generate some data, and `jobC` performs some analysis on that
+data. It wouldn't do for `jobC` to go firing off as soon as there was
+a free node, if there was no data available yet to analyze. We can
+deal with *dependencies* like these by passing a `-W
+depend=<dependency-list>` option to `qsub`. The dependency list can
+get pretty fancy (see `man qsub`), but for the case outlined above,
+we'll only need `afterany` dependencies (because `jobC` should execute
+after jobs `A` and `B`).
+
+Looking at the `man` page, the proper format for our dependency list
+is `afterany:jobid[:jobid...]`, so we need to catch the job IDs output
+by `qsub`. We'll use [[Bash's|Bash]] command substitution
+(`$(command)`) for this.
+
+ $ AID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && echo \"we're in\" > A_out" | qsub)
+ $ BID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && pwd > B_out" | qsub)
+ $ COND="depend=afterany:$AID:$BID -o C_out -W depend=afterany:$AID:$BID"
+ $ CID=$(echo "cd \$PBS_O_WORKDIR && cat A_out B_out" | qsub -W depend=afterany:$AID:$BID -o C_out)
+ $ echo -e "A: $AID\nB: $BID\nC: $CID"
+ A: 2712.n0.physics.drexel.edu
+ B: 2713.n0.physics.drexel.edu
+ C: 2714.n0.physics.drexel.edu
+ $ qstat
+ Job id Name User Time Use S Queue
+ ------------------------- ---------------- --------------- -------- - -----
+ 2712.n0 STDIN sysadmin 0 R batch
+ 2713.n0 STDIN sysadmin 0 R batch
+ 2714.n0 STDIN sysadmin 0 H batch
+ … time passes …
+ $ cat C_out
+ we're in
+ /home/sysadmin/howto/cluster/pbs_queues
+
+Note that we have to escape the `PBS_O_WORKDIR` expansion so that the
+variable substitution occurs when the job runs, and not when the echo
+command runs.
+
+Job arrays
+----------
+
+If you have *lots* of jobs you'd like to submit at once, it is tempting try
+
+ $ for i in $(seq 1 5); do JOBID=`echo "echo 'Running a job...'" | qsub`; done
+
+This does work, but it puts quite a load on the server as the number
+of jobs gets large. In order to allow the execution of such repeated
+commands the batch server provides *job arrays*. You simply pass
+`qsub` the `-t array_request` option, listing the range or list of IDs
+for which you'd like to run your command.
+
+ $ echo "sleep 30 && echo 'Running job \$PBS_ARRAYID...'" | qsub -t 1-5
+ 2721.n0.physics.drexel.edu
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2721-1.n0 STDIN-1 sysadmin 0 R batch
+ 2721-2.n0 STDIN-2 sysadmin 0 R batch
+ 2721-3.n0 STDIN-3 sysadmin 0 R batch
+ 2721-4.n0 STDIN-4 sysadmin 0 R batch
+ 2721-5.n0 STDIN-5 sysadmin 0 R batch
+
+One possibly tricky issue is depending on a job array. If you have an
+analysis job that you need to run to compile the results of your whole
+array, try
+
+ $ JOBID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && pwd && echo 1 > val\${PBS_ARRAYID}_out" | qsub -t 1-5)
+ $ sleep 2 # give the job a second to load in...
+ $ JOBNUM=$(echo $JOBID | cut -d. -f1)
+ $ COND="depend=afterany"
+ $ for i in $(seq 1 5); do COND="$COND:$JOBNUM-$i"; done
+ $ echo "cd \$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
+ qsub -o sum_out -W $COND
+ 2723.n0.physics.drexel.edu
+
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2722-1.n0 STDIN-1 sysadmin 0 R batch
+ 2722-2.n0 STDIN-2 sysadmin 0 R batch
+ 2722-3.n0 STDIN-3 sysadmin 0 R batch
+ 2722-4.n0 STDIN-4 sysadmin 0 R batch
+ 2722-5.n0 STDIN-5 sysadmin 0 R batch
+ 2723.n0 STDIN sysadmin 0 H batch
+ $ cat sum_out
+ 5
+
+Note that you must create any files needed by the dependent jobs
+*during* the early jobs. The dependent job may start as soon as the
+early jobs finish, *before* the `stdin` and `stdout` files for some
+early jobs have been written. Sadly, depending on either the returned
+job ID or just its numeric portion doesn't seem to work.
+
+It is important that the jobs on which you depend are loaded into the
+server *before your depending job is submitted*. To ensure this, you
+may need to add a reasonable sleep time between submitting your job
+array and submitting your dependency. However, your depending job
+will also hang if some early jobs have *already finished* by the time
+you get around to submitting it. In practice, this is not much of a
+problem, because your jobs will likely be running for at least a few
+minutes, giving you a large window during which you can submit your
+dependent job.
+
+See the examples sections and `man qsub` for more details.
+
+<a name="qstat" />
+
+Querying
+========
+
+You can get information about currently running and queued jobs with
+`qstat`. In the examples in the other sections, we've been using bare
+`qstat`s to get information about the status of jobs in the queue.
+You get information about a particular command with
+
+ $ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
+ $ sleep 2 && qstat $JOBID
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2724.n0 STDIN sysadmin 0 R batch
+
+and you can get detailed information on a every command (or a
+particular one, see previous example) with the `-f` (full) option.
+
+ $ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
+ $ sleep 2
+ $ qstat -f
+ Job Id: 2725.n0.physics.drexel.edu
+ Job_Name = STDIN
+ Job_Owner = sysadmin@n0.physics.drexel.edu
+ job_state = R
+ queue = batch
+ server = n0.physics.drexel.edu
+ Checkpoint = u
+ ctime = Thu Jun 26 13:58:54 2008
+ Error_Path = n0.physics.drexel.edu:/home/sysadmin/STDIN.e2725
+ exec_host = n8/0
+ Hold_Types = n
+ Join_Path = n
+ Keep_Files = n
+ Mail_Points = a
+ mtime = Thu Jun 26 13:58:55 2008
+ Output_Path = n0.physics.drexel.edu:/home/sysadmin/STDIN.o2725
+ Priority = 0
+ qtime = Thu Jun 26 13:58:54 2008
+ Rerunable = True
+ Resource_List.nodect = 1
+ Resource_List.nodes = 1
+ Resource_List.walltime = 01:00:00
+ session_id = 18020
+ Variable_List = PBS_O_HOME=/home/sysadmin,PBS_O_LANG=en_US.UTF-8,
+ PBS_O_LOGNAME=sysadmin,
+ PBS_O_PATH=/home/sysadmin/bin:/usr/local/bin:/usr/local/sbin:/usr/bin
+ :/usr/sbin:/bin:/sbin:/usr/X11R6/bin:/usr/local/maui/bin:/home/sysadmi
+ n/script:/home/sysadmin/bin:.,PBS_O_MAIL=/var/mail/sysadmin,
+ PBS_O_SHELL=/bin/bash,PBS_SERVER=n0.physics.drexel.edu,
+ PBS_O_HOST=n0.physics.drexel.edu,
+ PBS_O_WORKDIR=/home/sysadmin/,
+ PBS_O_QUEUE=batch
+ etime = Thu Jun 26 13:58:54 2008
+ start_time = Thu Jun 26 13:58:55 2008
+ start_count = 1
+
+The `qstat` command gives you lots of information about the current
+state of a job, but to get a history you should use the `tracejob`
+command.
+
+ $ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
+ $ sleep 2 && tracejob $JOBID
+
+ Job: 2726.n0.physics.drexel.edu
+
+ 06/26/2008 13:58:57 S enqueuing into batch, state 1 hop 1
+ 06/26/2008 13:58:57 S Job Queued at request of sysadmin@n0.physics.drexel.edu, owner = sysadmin@n0.physics.drexel.edu, job name = STDIN, queue = batch
+ 06/26/2008 13:58:58 S Job Modified at request of root@n0.physics.drexel.edu
+ 06/26/2008 13:58:58 S Job Run at request of root@n0.physics.drexel.edu
+ 06/26/2008 13:58:58 S Job Modified at request of root@n0.physics.drexel.edu
+
+You can also get the status of the queue itself by passing `-q` option to `qstat`
+
+ $ qstat -q
+
+ server: n0
+
+ Queue Memory CPU Time Walltime Node Run Que Lm State
+ ---------------- ------ -------- -------- ---- --- --- -- -----
+ batch -- -- -- -- 2 0 -- E R
+ ----- -----
+ 2 0
+
+or the status of the server with the `-B` option.
+
+ $ qstat -B
+ Server Max Tot Que Run Hld Wat Trn Ext Status
+ ---------------- --- --- --- --- --- --- --- --- ----------
+ n0.physics.drexe 0 2 0 2 0 0 0 0 Active
+
+You can get information on the status of the various nodes with
+`qnodes` (a symlink to `pbsnodes`). The output of `qnodes` is bulky
+and not of public interest, so we will not reproduce it here. For
+more details on flags you can pass to `qnodes`/`pbsnodes` see `man
+pbsnodes`, but I haven't had any need for fancyness yet.
+
+<a name="qalter" />
+
+Altering and deleting jobs
+==========================
+
+Minor glitches in submitted jobs can be fixed by altering the job with `qalter`.
+For example, incorrect dependencies may be causing a job to hold in the queue forever.
+We can remove these invalid holds with
+
+ $ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub -W depend=afterok:3)
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2725.n0 STDIN sysadmin 0 R batch
+ 2726.n0 STDIN sysadmin 0 R batch
+ 2727.n0 STDIN sysadmin 0 H batch
+ $ qalter -h n $JOBID
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2725.n0 STDIN sysadmin 0 R batch
+ 2726.n0 STDIN sysadmin 0 R batch
+ 2727.n0 STDIN sysadmin 0 Q batch
+
+`qalter` is a Swiss-army-knife command, since it can change many
+aspects of a job. The specific hold-release case above could also
+have been handled with the `qrls` command. There are a number of
+other `q*` commands which provide detailed control over jobs and
+queues, but I haven't had to use them yet.
+
+If you decide a job is beyond repair, you can kill it with `qdel`.
+For obvious reasons, you can only kill your own jobs, unless your an
+administrator.
+
+ $ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
+ $ qdel $JOBID
+ $ echo "deleted $JOBID"
+ deleted 2728.n0.physics.drexel.edu
+ $ qstat
+ Job id Name User Time Use S Queue
+ ----------------- ---------------- --------------- -------- - -----
+ 2725.n0 STDIN sysadmin 0 R batch
+ 2726.n0 STDIN sysadmin 0 R batch
+ 2727.n0 STDIN sysadmin 0 R batch
+
+Further reading
+===============
+
+I used to have a number of scripts and hacks put together to make it
+easy to run my [[sawsim]] Monte Carlo simulations and setup dependent
+jobs to process the results. This system was never particularly
+elegant. Over time, I gained access to a number of SMP machines, as
+well as my multi host cluster. In order to support more general
+parallelization and post-processing, I put together a general manager
+for embarassingly parallel jobs. There are implementations using a
+range of parallelizing tools, from multi-threading through PBS and
+MPI. See the [sawsim source][sawsim-manager] for details.
+
+
+[sec.qsub]: #qsub
+[sec.qstat]: #qstat
+[sec.qalter]: #qalter
+[sawsim-manager]: http://git.tremily.us/?p=sawsim.git;a=tree;f=pysawsim/manager;hb=HEAD
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-we're in
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-# each MetaPost graphic has it's own file,
-# so the basic definitions should get bundled out into an external file
-# (encourages reuse anyway, so it's good for you :p)
-
-all: main.pdf
-
-view: all
- xpdf main.pdf &
-
-latex-clean:
- rm -f *.1 *.log *.mp *.mpx *.aux *.out *.cut
-
-semi-clean: latex-clean
- rm -f command_list *.sh_out *.[eo][0-9]* *_out *_err comE comO
-
-pdf-clean:
- rm -f *.pdf
-
-clean: semi-clean pdf-clean
-
-%.pdf: %.tex *.tex dummy.sh_out
- pdflatex $<
- pdflatex $<
-
-command_list: make_command_list.sh submitting.tex querying.tex altering.tex
- ./$^ > $@
-
-dummy.sh_out: make_com_out.sh command_list
- ./$<
- echo "dummy dependency for makefile" > $@
+++ /dev/null
-Running a job...
+++ /dev/null
-/home/sysadmin
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-Running a job...
-
-real 0m30.010s
-user 0m0.000s
-sys 0m0.000s
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-/home/sysadmin
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-Running a job...
-
-real 0m30.013s
-user 0m0.000s
-sys 0m0.000s
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-Running job $PBS_ARRAYID...
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-\section{Altering and deleting jobs}
-\label{sec.qalter}
-
-Minor glitches in submitted jobs can be fixed by altering the job with |qalter|.
-For example, incorrect dependencies may be causing a job to hold in the queue forever.
-We can remove these invalid holds with
-\qcom{qalter_depend_echo.sh}
-|qalter| is a Swiss-army-knife-style command, since it can change many aspects of a job.
-The specific hold-release case above could also have been handled with the |qrls| command.
-There are a number of |q*| commands which provide a
-
-If you decide a job is beyond repair, you can kill it with |qdel|.
-For obvious reasons, you can only kill your own jobs, unless your an administrator.
-\qcom{qdel_echo.sh}
+++ /dev/null
-JOBID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && pwd && echo 1 > val\\\${PBS_ARRAYID}_out" | qsub -t 1-5`
-sleep 2 # give the Job a second to load in...
-#echo "cd \\\$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
-# qsub -o sum_out -W depend=afterany:$JOBID
-JOBNUM=`echo $JOBID | cut -d. -f1`
-#echo "cd \\\$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
-# qsub -o sum_out -W depend=afterany:$JOBNUM
-COND="depend=afterany"
-i=1
-while [ $i -le 5 ]
-do
- COND="$COND:$JOBNUM-$i"
- let "i += 1"
-done
-echo "cd \$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
- qsub -o sum_out -W $COND
+++ /dev/null
-$ JOBID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && pwd && echo 1 > val\\\${PBS_ARRAYID}_out" | qsub -t 1-5`
-$ sleep 2 # give the Job a second to load in...
-$ #echo "cd \\\$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
-$ # qsub -o sum_out -W depend=afterany:$JOBID
-$ JOBNUM=`echo $JOBID | cut -d. -f1`
-$ #echo "cd \\\$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
-$ # qsub -o sum_out -W depend=afterany:$JOBNUM
-$ COND="depend=afterany"
-$ i=1
-$ while [ $i -le 5 ]
-$ do
-> COND="$COND:$JOBNUM-$i"
-> let "i += 1"
-> done
-$ echo "cd \$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
-> qsub -o sum_out -W $COND
-2723.n0.physics.drexel.edu
+++ /dev/null
-$ cat sum_out
-5
+++ /dev/null
-echo "sleep 30 && echo 'Running job \$PBS_ARRAYID...'" | qsub -t 1-5
+++ /dev/null
-$ echo "sleep 30 && echo 'Running job \$PBS_ARRAYID...'" | qsub -t 1-5
-2721.n0.physics.drexel.edu
+++ /dev/null
-QCOM simple_echo.sh
-COM qstat_simple_echo qstat
-QCOM simple_script.sh
-sleep 40
-QCOM named_echo.sh
-COM qstat_named_echo qstat
-QCOM explicit_oe_echo.sh
-sleep 2
-COM explicit_oe_echo_o cat my_out
-COM explicit_oe_echo_e cat my_err
-sleep 40
-QCOM workdir_echo.sh
-sleep 2
-COMOUT
-QCOM get_walltime_echo.sh
-sleep 40
-COMOUT
-QCOM set_walltime_echo.sh
-sleep 2
-COM qstat_set_walltime_echo qstat -f | grep '[.]walltime'
-sleep 38
-QCOM depend_echo.sh
-sleep 2
-COM qstat_depend_echo qstat
-sleep 50
-COM depend_echo_out cat C_out
-QCOM while_echo.sh
-sleep 10
-QCOM array_echo.sh
-sleep 2
-COM qstat_array_echo qstat
-sleep 50
-QCOM array_depend_echo.sh
-sleep 2
-COM qstat_array_depend_echo qstat
-sleep 60
-COM array_depend_echo_out cat sum_out
-QCOM qstat_particular_echo.sh
-sleep 40
-QCOM qstat_full_echo.sh
-QCOM tracejob_echo.sh
-COM qstat_queue_info qstat -q
-COM qstat_server_info qstat -B
-QCOM qalter_depend_echo.sh
-QCOM qdel_echo.sh
+++ /dev/null
-AID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && echo \"we're in\" > A_out" | qsub`
-BID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && pwd > B_out" | qsub`
-COND="depend=afterany:$AID:$BID -o C_out -W depend=afterany:$AID:$BID"
-CID=`echo "cd \\\$PBS_O_WORKDIR && cat A_out B_out" | \
- qsub -W depend=afterany:$AID:$BID -o C_out`
-echo -e "A: $AID\nB: $BID\nC: $CID"
+++ /dev/null
-$ AID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && echo \"we're in\" > A_out" | qsub`
-$ BID=`echo "cd \\\$PBS_O_WORKDIR && sleep 30 && pwd > B_out" | qsub`
-$ COND="depend=afterany:$AID:$BID -o C_out -W depend=afterany:$AID:$BID"
-$ CID=`echo "cd \\\$PBS_O_WORKDIR && cat A_out B_out" | \
-> qsub -W depend=afterany:$AID:$BID -o C_out`
-$ echo -e "A: $AID\nB: $BID\nC: $CID"
-A: 2712.n0.physics.drexel.edu
-B: 2713.n0.physics.drexel.edu
-C: 2714.n0.physics.drexel.edu
+++ /dev/null
-$ cat C_out
-we're in
-/home/sysadmin/howto/cluster/pbs_queues
+++ /dev/null
-dummy dependency for makefile
+++ /dev/null
-#!/bin/bash
-# file: echo_script.sh
-sleep 30
-echo "a really,"
-echo "really,"
-echo "complicated"
-echo "script"
+++ /dev/null
-a really,
-really,
-complicated
-script
+++ /dev/null
-a really,
-really,
-complicated
-script
+++ /dev/null
-\section{Example 1: jobs depending on jobs}
-\label{sec.example1}
-
-As an example of a medium-complexity compound job, consider my single-proccessor Monte Carlo with two layers of post processing batch submission script.
-The simulation program is the compiled binary |sawsim| which models the unfolding of a multi-domain protein.
-It takes command line arguments specifying model parameters and experimental conditions and prints the forces at which the various domains unfold to |stdout|.
-I want to run with a certain set of parameters, but sweep one of the parameters (pulling velocity) through a number of different values.
-For each basic-parameter--pulling-velocity combination, I want to run the simulation 400 times, to get statistically significant output.
-The first stage of the post-processing gathers the output of all the |sawsim| jobs into a single list of unfolding forces at each velocity.
-The second stage of the post-processing generates histograms of unfolding forces for each velocity and a file with pulling speed vs.\ unfolding force data for plotting.
-\inputfile{run_vel_dist.sh}{run\_vel\_dist.sh}
-We start off by generating and |cd|ing into a new directory, since we'll be generating \emph{lots} of files.
-Then we loop through our velocities, creating a new job array (|sawsim|) executing |sawsim| with the appropriate parameters.
-
-Job arrays are still young in Torque (our batch queue manager), and we can't depend on the job array as a whole.
-Because the number of jobs we can depend on simultaneously is limited (command line size?), we bundle several |sawsim| executions into a single array job instance.
-This allows us to keep the number of executions up without generating huge dependency lists for the analysis jobs.
-We add job array with a user hold (|-h|) to ensure that the jobs don't begin executing immediately and exit before we start our analysis jobs.
-We also sleep for a few seconds after adding the job, because sometimes the array takes a bit to `deploy' into the queue (symptom: out-of-order job IDs in the queue).
-
-The first postprocessing stage (|sawComp|) gathers the output from the array job for it's particular velocity, strips comment lines, and dumps the output into a central file (|data\_\$V|).
-We set this job to depend on each of the array job instances at that velocity (since we can't depend on the entire array job).
-We also start \emph{this} job on hold, so that it doesn't exit before we add the second layer analysis job.
-After adding the job, we release the user holds on the array job instances to let them get going (another place where access by array job ID would be nice\ldots).
-
-The final analysis stage involves enough steps that it has it's own script, but nothing in that script involves the batch queue system, so it is not reproduced here.
-We depend on all the first stage analysis jobs, since we need the consolidated |data\_\$V| files for the script.
-There is no need to hold this job, since nothing depends on it.
-After adding the job, we release the \emph{user} holds on the first-stage analysis jobs.
-The \emph{system} holds due to their dependencies remain until they are satisfied as the |sawsim| jobs complete.
+++ /dev/null
-echo "echo 'ABC' && echo 'DEF' > /dev/stderr" | qsub -o my_out -e my_err
+++ /dev/null
-$ echo "echo 'ABC' && echo 'DEF' > /dev/stderr" | qsub -o my_out -e my_err
-2708.n0.physics.drexel.edu
+++ /dev/null
-$ cat my_err
-DEF
+++ /dev/null
-$ cat my_out
-ABC
+++ /dev/null
-# .procmailrc
-#
-# log recipt of mail from PBS queue administrator from your system mailbox
-#
-# see man procmail, procmailrc, and procmailex
-# there is also a good procmail tutorial at
-# http://userpages.umbc.edu/~ian/procmail.html
-#
-# procmail uses sed-like regexps
-
-DEFAULT=$MAIL
-MAILDIR=$HOME/.mailspool
-LOGFILE=$MAILDIR/mailfilter/procmailrc.log
-SHELL=/bin/bash
-COMPLETED=$MAILDIR/completed
-
-# log job id's and exit status for anything satifying ALL of
-# From adm@abax.physics.drexel.edu,
-# Envelope-to: sysadmin@n0.abax.physics.drexel.edu
-# To: sysadmin@n0.abax.physics.drexel.edu
-# Subject: PBS JOB [0-9]*.n0.abax.physics.drexel.edu
-# lock the mail file while the processing is being carried out
-:0 b: # b only use the body, (c pass copy to other rules), : use a lockfile
-* ^From adm@abax[.]physics[.]drexel[.]edu
-* ^To: sysadmin@n0[.]abax[.]physics[.]drexel[.]edu
-* ^Subject: PBS JOB [0-9]*[.]n0[.]abax[.]physics[.]drexel[.]edu
-| cat >> $COMPLETED
+++ /dev/null
-#!/bin/bash
-#
-# override Torque qsub's strange environment shelving behavior by copying all
-# your precious environmental variables back to where they should be.
-#
-# usage: source dup_env
-
-while read VARSTR
- do
- VAR=${VARSTR%=*} # strip everything after & including the =
- VAL=${VARSTR#$VAR=} # strip everying up & including to the =
- #echo "parsed '$VARSTR' to '$VAR' & '$VAL'"
- if [ "${VAR:0:6}" == "PBS_O_" ]
- then
- ORIGVAR=${VAR#PBS_O_} # strip PBS_O_ from $VAR
- if [ "${!ORIGVAR}" != "$VAL" ] && [ "$ORIGVAR" != "HOST" ]
- then
- #echo "changing $ORIGVAR from '${!ORIGVAR}' to '$VAL'"
- export $ORIGVAR=$VAL
- fi
- fi
-done < <(printenv)
+++ /dev/null
-#!/bin/bash
-#
-# Running my qcmd implementation on your system mailbox can quickly fill it up
-# with PBS junk. This scans through the box and deletes any messages from the
-# PBS admin.
-#
-# from man procmail:
-# Procmail can also be invoked to postprocess an already filled system mailbox.
-# ...
-#
-# This script is almost verbatim from 'man procmail'
-
-ORIGMAILS="$MAIL $HOME/.mailspool/completed"
-FILTER=$HOME/.mailspool/mailfilter/qcleanmail.proc
-
-clean ()
-{
- ORIGMAIL=$1
- if cd $HOME &&
- test -s $ORIGMAIL &&
- lockfile -r0 -l1024 .newmail.lock 2>/dev/null
- then
- umask 077
- trap "rm -f .newmail.lock" 1 2 3 13 15
- echo "cleaning $ORIGMAIL"
- # lock the system maildir, and extract all the messages
- lockfile -l1024 -ml
- cat $ORIGMAIL >>.newmail &&
- cat /dev/null >$ORIGMAIL
- lockfile -mu
- # lock released, now new messages can arrive as they normally do
-
- # process the mail we copied out with our filter
- # mail that should be in $ORIGMAIL will be appended as procmail notices...
- formail -s procmail $FILTER <.newmail &&
- rm -f .newmail
- rm -f .newmail.lock
- fi
- return 0
-}
-
-for M in $ORIGMAILS
- do
- clean $M
-done
-
-exit 0
+++ /dev/null
-# qcleanmail.proc
-#
-# remove mail from PBS queue administrator from your system mailbox
-#
-# see man procmail, procmailrc, and procmailex
-# there is also a good procmail tutorial at
-# http://userpages.umbc.edu/~ian/procmail.html
-#
-# procmail uses sed-like regexps
-
-MAILDIR=$HOME/.mailspool #$MAIL
-LOGFILE=$MAILDIR/mailfilter/qcleanmail.log
-SHELL=/bin/bash
-HOST=`hostname -f`
-PBS_ADM=adm@abax[.]physics[.]drexel[.]edu
-
-# trash anything from satifying ALL of
-# From adm@abax.physics.drexel.edu,
-# Envelope-to: $USER@$HOST
-# To: $USER@$HOST
-# Subject: PBS JOB [0-9]*.$HOST
-# lock the mail file while the processing is being carried out
-:0: # the last colon means use a lockfile
-* ^From $PBS_ADM
-* ^To: $USER@$HOST
-* ^Subject: PBS JOB [0-9]*$HOST
-/dev/null # write matching messages to /dev/null
+++ /dev/null
-#!/bin/bash
-#
-# Run commands through a PBS queue without having to remember anything. :p
-#
-# This script keeps stdin and stdout open until the PBS job returns, monitoring
-# your email for the appropriate job-completion message from the PBS server.
-# This lets you bump a long-executing task onto a compute node, while keeping
-# the lightweight part of your processing on the master node, for easier
-# connection and dependency checking.
-#
-# Downsides to the current implementation:
-# Blocks on email with a subshell (the piped input while loop) and tail
-# running, so counting the script itself, that's 3 processes on the head node
-# for each PBS job you're waiting for. While that's not a really big deal for
-# a few dozen jobs, it eats up memory fairly quickly for thousands of jobs.
-#
-# Another drawback is that you can only append to your $MAIL file while this is
-# running. I'm using a .procmailrc file to deflect PBS-related mail to a
-# seperate mailbox, so I can still edit my system mailbox while this script is
-# running, but that's one more thing you'd have to set up...
-#
-# Yet another drawback is that you can't run qsub from a screen session, but
-# that is just qsub in general. Sigh.
-#
-# The solution to the memory problem is to have a single script handle all
-# the spawning and waiting for multiple commands. Take a look at 'qcmds'
-#
-# usage: qcmd [-w[[H:]M:]S] command [arguments]
-# where -w optionally sets the wall time
-# for example:
-# $ ls .
-# file
-# $ qcmd cp file file2 && ls .
-# file
-# file2
-# $ diff file file2
-# (none)
-# or
-# $ qcmd pwd '&&' echo \$PBS_O_WORKDIR
-# /home/sysadmin/script
-# /home/sysadmin/script
-# and to prove we're running through qsub (2nd hostname is on calling system)
-# $ qcmd hostname && hostname
-# n8
-# n0
-#
-# Warning:
-# This script uses process substitution which is a non-POSIX bash feature.
-#
-# command line arguments
-# |
-# v
-# addjob() ---(submit job with qsub)---> Job-Queue
-# | |
-# +----+ (job-complete email)
-# | |
-# while: v |
-# checkfornew() v
-# getnextmail() <---(tail -f $MAIL)--- Mailbox
-
-DEBUG=0
-MAIL=$HOME/.mailspool/completed
-# I have a ~/.procmailrc filter forwarding my PBS mail bodies to this $MAIL
-# If you don't, comment the line out so you monitor your system $MAIL.
-
-JOB_OUTSTANDING= # Store the job id of our uncompleted job
-MAIL_BODY="" # Store the return of getnextmail()
-
-if [ $DEBUG -eq 1 ]
- then
- DEBUGFILE=qcmd.$$
- > $DEBUGFILE # clear $DEBUGFILE if it existed before (Warning: clobber)
-else
- DEBUGFILE=/dev/null
-fi
-
-# functions for job spawning
-
-addjob ()
-{
- CMMD=$*
- echo running: $CMMD >> $DEBUGFILE
- SCRIPT="cd \$PBS_O_WORKDIR && source dup_env && $CMMD"
- # dup_env is in ~/bin even though it's a script
- # since qsub creates it's own evironment, and moves X -> PBS_O_X
- # for example, PATH -> PBS_O_PATH.
- # who knows why it does this...
- JOBID=`echo $SCRIPT | qsub -mae $WALLTIME_OPTION || exit 1`
- # -mae : Send mail on abort or execute
- #JOBNAME=STDIN # the qsub default for scripts piped into qsub
- echo spawner: started $JOBID >> $DEBUGFILE
- JOB_OUTSTANDING="$JOBID"
- echo "add new depend: $JOBID" >> $DEBUGFILE
- return 0
-}
-
-# functions for the job checking loop
-
-# look for completion message bodies along the lines of:
-# PBS Job Id: 206.n0.abax.physics.drexel.edu
-# Job Name: STDIN
-# ...
-# <-- blank line
-#
-# could also poll on ls.
-# neither 'ls' or 'tail -f' busy loops seem to take measurable processor time.
-getnextmail() # blocking, fd 3 is tail -f $MAIL output
-{
- BODY=""
- DONE=0
- INJOB=0
- echo "block on mail" >> $DEBUGFILE
- while [ $DONE -eq 0 ] && read LINE <&3
- do
- if [ "${LINE:0:11}" == "PBS Job Id:" ]
- then
- # we're reading an email about a job.
- #echo "in a job" >> $DEBUGFILE
- INJOB=1
- fi
- if [ $INJOB -eq 1 ]
- then
- #echo "getting mail: $LINE" >> $DEBUGFILE
- if [ "${#LINE}" -eq 0 ]
- then
- #echo "matched blank line" # we're leaving the email about our job.
- #echo "got mail" >> $DEBUGFILE
- DONE=1
- break
- fi
- BODY=`echo -e "$BODY\n$LINE"`
- fi
- done
- echo "returning mail" >> $DEBUGFILE
- MAIL_BODY="$BODY"
- return 0
-}
-
-check4done()
-{
- JOBID=$1
- i=0
- echo -n "were we waiting on $JOBID? " >> $DEBUGFILE
- if [ "$JOBID" == "$JOB_OUTSTANDING" ]
- then
- # Sometimes the email comes in BEFORE STDOUT and STDERR were written
- # stupid Torque...
- JOBNUM=`echo "$JOBID" | sed 's/[.].*//'`
- JOBNAME=STDIN # the qsub default for scripts piped into qsub
- STDOUT=$JOBNAME.o$JOBNUM
- STDERR=$JOBNAME.e$JOBNUM
- while [ ! -e "$STDOUT" ] || [ ! -e "$STDERR" ]
- do
- sleep 0
- done
- # end stupid Torque hack
-
- echo "yes" >> $DEBUGFILE
- return 0 # job complete :)
- fi
- echo "no" >> $DEBUGFILE
- return 1 # not one of our completing jobs
-}
-
-printjoboutput()
-{
- JOBID=$1
- shift
- MAIL_BODY=$*
-
- JOBNUM=`echo "$JOBID" | sed 's/[.].*//'`
- JOBNAME=STDIN # the qsub default for scripts piped into qsub
- STDOUT=$JOBNAME.o$JOBNUM
- STDERR=$JOBNAME.e$JOBNUM
-
- cat $STDOUT
- cat $STDERR >&2
- rm -f $STDOUT $STDERR
-
- return 0
-}
-
-
-echo "spawning job" >> $DEBUGFILE
-
-if [ ${1:0:2} == "-w" ]
-then
- WALLTIME=${1:2}
- WALLTIME_OPTION="-l walltime=$WALLTIME"
- shift
-fi
-
-addjob $*
-
-# use process substitution to keep tail running between reads, see 'man bash'
-exec 3< <(tail -f $MAIL --pid $$) # open the MAIL file for reading on fd 3
-# $$ expands to this script's PID
-# --pid $$ sets up tail to die when this script exits, see 'man tail'
-
-echo "loop on outstanding job" >> $DEBUGFILE
-
-# email checking loop, in the forground
-while [ -n "$JOB_OUTSTANDING" ]
- do
- getnextmail
- JOBID=`echo "$MAIL_BODY" | sed -n 's/PBS Job Id: *//p'`
- if check4done "$JOBID"
- then
- printjoboutput $JOBID "$MAIL_BODY"
- EXIT=`echo "$BODY" | sed -n 's/Exit_status=//p'`
- unset JOB_OUTSTANDING
- fi
-done
-
-# the tail dies automatically because of the --pid argument
-# we'll leave the tail file descriptor open just in case
-# tail tries to print something else before it dies.
-
-echo "qcmd complete" >> $DEBUGFILE
-
-exit $EXIT
+++ /dev/null
-#!/bin/bash
-#
-# Run commands through a PBS queue without having to remember anything. :p
-#
-# This is an attempt to scale qcmd functionality to multiple commands.
-# The goal is to be able to spawn a bunch of PBS jobs from the command line or
-# a script, and then wait until they all finish before carrying on. Basically
-# the bash 'wait' functionality for background commands, except for PBS jobs
-# spawned by your particular process.
-#
-# This script doesn't bother with keeping stdin and stdout open for each job,
-# since that could be a lot of file descriptors. It also doesn keep a process
-# going for each job. Instead, we fire up qcmds in the backround attached to
-# an input and output fifo. New job commands get piped into the input fifo,
-# and job completion information gets piped out the output fifo. When all the
-# jobs that qcmds has started have completed, qcmds closes it's output fifo.
-#
-# qcmds uses endlines ('\n') as it's job-delimiters when reading it's input,
-# so you can only use single-line jobs. They can be long lines though ;).
-#
-# Simple usage would be:
-# echo 'sleep 5 && echo hi there' | qcmds
-# Common usage would be:
-# #!/bin/bash
-# i=0
-# $QCMDS=$((while [ $i -lt 1000 ]
-# do
-# echo "sleep 10 && echo $i"
-# let "i += 1"
-# done
-# ) | qcmds)
-# wait # wait for qcmds tail to finish
-# exit 0
-#
-# Downsides to the current implementation:
-# You can only append to your $MAIL file while this is running. I'm using a
-# .procmailrc file to deflect PBS-related mail to a seperate mailbox, so I can
-# still edit my system mailbox while this script is running, but that's one
-# more thing you'd have to set up...
-#
-# Another drawback is that you can't run qsub from a screen session, but that
-# is just qsub in general. Sigh.
-#
-# For small numbers of jobs where the scripting overhead of a seperate process
-# and fifos seems excessive, take a look at the more memory intensive 'qcmd'.
-#
-# For a nice introduction to bash arrays, see
-# http://tldp.org/LDP/abs/html/arrays.html
-#
-# see ~/script/.test/t_fifo_readline for a demonstration of the `threading'
-#
-# Warning:
-# This script uses process substitution which is a non-POSIX bash feature.
-#
-# stdin
-# |
-# (list of jobs)
-# |
-# v
-# addjob() ---(submit job with qsub)---> Job-Queue
-# | |
-# +----+ (job-complete email)
-# | |
-# while: v |
-# checkfornew() v
-# getnextmail() <---(tail -f $MAIL)--- Mailbox
-
-DEBUG=0
-MAIL=$HOME/.mailspool/completed
-# I have a ~/.procmailrc filter forwarding my PBS mail bodies to this $MAIL
-# If you don't, comment the line out so you monitor your system $MAIL.
-
-JOBS_OUTSTANDING=( ) # Store job ids that haven't completed yet
-NUM_OUTSTANDING=0
-MAIL_BODY="" # Store the return of getnextmail()
-
-if [ $DEBUG -eq 1 ]
- then
- DEBUGFILE=qcmds.$$
- > $DEBUGFILE # clear $DEBUGFILE if it existed before (Warning: clobber)
-else
- DEBUGFILE=/dev/null
-fi
-
-# functions for the job spawning subshell
-
-addjob ()
-{
- CMMD=$*
- echo running: $CMMD >> $DEBUGFILE
- SCRIPT="cd \$PBS_O_WORKDIR && source dup_env && $CMMD"
- # dup_env is in ~/bin even though it's a script
- # since qsub creates it's own evironment, and moves X -> PBS_O_X
- # for example, PATH -> PBS_O_PATH.
- # who knows why it does this...
- JOBID=`echo $SCRIPT | qsub -mae || exit 1`
- # -mae : Send mail on abort or execute
- #JOBNAME=STDIN # the qsub default for scripts piped into qsub
- echo spawner: started $JOBID >> $DEBUGFILE
- echo $JOBID # >> $SPAWN_TO_CHECK
- return 0
-}
-
-# functions for the job checking loop
-
-check4new() # blocks for < 1 second, fd 3 is addjob() output
-{
- read -t1 JOBID <&3 || return 1 # nothing new.
- # add job to our outstanding list
- JOBNUM=`echo "$JOBID" | sed 's/[.].*//'`
- JOBS_OUTSTANDING[$JOBNUM]=1
- let "NUM_OUTSTANDING += 1"
- echo "add new depend: $JOBID" >> $DEBUGFILE
- # extra space ': $J' to align with addjob DEBUG message
- return 0
-}
-
-
-# look for completion message bodies along the lines of:
-# PBS Job Id: 206.n0.abax.physics.drexel.edu
-# Job Name: STDIN
-# ...
-# <-- blank line
-#
-# could also poll on ls.
-# neither 'ls' or 'tail -f' busy loops seem to take measurable processor time.
-getnextmail() # blocking, fd 4 is tail -f $MAIL output
-{
- BODY=""
- DONE=0
- INJOB=0
- echo "block on mail" >> $DEBUGFILE
- while [ $DONE -eq 0 ] && read LINE <&4
- do
- if [ "${LINE:0:11}" == "PBS Job Id:" ]
- then
- # we're reading an email about a job.
- #echo "in a job" >> $DEBUGFILE
- INJOB=1
- fi
- if [ $INJOB -eq 1 ]
- then
- #echo "getting mail: $LINE" >> $DEBUGFILE
- if [ "${#LINE}" -eq 0 ]
- then
- #echo "matched blank line" # we're leaving the email about our job.
- #echo "got mail" >> $DEBUGFILE
- DONE=1
- break
- fi
- BODY=`echo -e "$BODY\n$LINE"`
- fi
- done
- echo "returning mail" >> $DEBUGFILE
- MAIL_BODY="$BODY"
- return 0
-}
-
-check4done()
-{
- JOBID=$1
- JOBNUM=`echo "$JOBID" | sed 's/[.].*//'`
- echo -n "were we waiting on $JOBID? " >> $DEBUGFILE
- if [ -n "${JOBS_OUTSTANDING[$JOBNUM]}" ]
- then
- echo "yes" >> $DEBUGFILE
- # Sometimes the email comes in BEFORE STDOUT and STDERR were written
- # stupid Torque...
- JOBNAME=STDIN # the qsub default for scripts piped into qsub
- STDOUT=$JOBNAME.o$JOBNUM
- STDERR=$JOBNAME.e$JOBNUM
- while [ ! -e "$STDOUT" ] || [ ! -e "$STDERR" ]
- do
- sleep 0
- done
- # end stupid Torque hack
- # remove the outstanding entry from the array.
- unset JOBS_OUTSTANDING[$JOBNUM]
- let "NUM_OUTSTANDING -= 1"
- return 0 # job complete :)
- fi
- echo "no" >> $DEBUGFILE
- return 1 # not one of our completing jobs
-}
-
-printjobinfo()
-{
- JOBID=$1
- shift
- MAIL_BODY=$*
-
- JOBNUM=`echo "$JOBID" | sed 's/[.].*//'`
- JOBNAME=STDIN # the qsub default for scripts piped into qsub
- STDOUT=$JOBNAME.o$JOBNUM
- STDERR=$JOBNAME.e$JOBNUM
-
- HOST=`echo "$BODY" | sed -n 's/Exec host: *//p'`
- EXIT=`echo "$BODY" | sed -n 's/Exit_status=//p'`
- WALLTIME=`echo "$BODY" | sed -n 's/resources_used.walltime=//p'`
- SESSION=`echo "$BODY" | sed -n 's/session_id=//p'`
-
- echo -e "$JOBID\t$JOBNUM\t$EXIT\t$STDOUT\t$STDERR\t$HOST\t$SESSION\t$WALLTIME"
- echo -e "$JOBID\t$JOBNUM\t$EXIT\t$STDOUT\t$STDERR\t$HOST\t$SESSION\t$WALLTIME" >> $DEBUGFILE
-
- return 0
-}
-
-nothing()
-{
- return 0
-}
-
-echo "start the spawning subshell" >> $DEBUGFILE
-
-# job-spawning subshell, in a subshell so we can't access it's variables
-# we send this script's stdin into the subshell as it's stdin (< /dev/stdin)
-# and we open the subshell's output for reading on file descriptor 3
-# with 'exec 3< <(subshell cmmsds)' (process substitution, see 'man bash').
-exec 3< <(
- echo "spawner: about to read" >> $DEBUGFILE
- while read LINE
- do
- addjob $LINE
- done
- exit 0
-) < /dev/stdin
-
-# use process substitution to keep tail running between reads, see 'man bash'
-exec 4< <(tail -f $MAIL --pid $$) # open the MAIL file for reading on fd 4
-# $$ expands to this script's PID
-# --pid $$ sets up tail to die when this script exits, see 'man tail'
-
-echo "loop on outstanding jobs" >> $DEBUGFILE
-
-# email checking loop, in the forground
-check4new # make sure there is an outstanding job first...
-while [ $NUM_OUTSTANDING -gt 0 ]
- do
- getnextmail
- while check4new; do nothing; done; # clean out the pipe
- JOBID=`echo "$MAIL_BODY" | sed -n 's/PBS Job Id: *//p'`
- if check4done "$JOBID"
- then
- printjobinfo $JOBID "$MAIL_BODY"
- fi
- echo "still $NUM_OUTSTANDING job(s) outstanding" >> $DEBUGFILE
-done
-
-wait
-
-echo "cleanup" >> $DEBUGFILE
-
-exec 3>&- # close the connection from the job-spawning subshell
-
-# the tail dies automatically because of the --pid argument
-# we'll leave the tail file descriptor open just in case
-# tail tries to print something else before it dies.
-
-echo "qcmds complete" >> $DEBUGFILE
-
-exit 0
+++ /dev/null
-echo "time (sleep 30 && echo 'Running a job...')" | qsub -j oe
+++ /dev/null
-$ echo "time (sleep 30 && echo 'Running a job...')" | qsub -j oe
-2710.n0.physics.drexel.edu
- ... time passes ...
-$ cat STDIN.o2710
-Running a job...
-
-real 0m30.013s
-user 0m0.000s
-sys 0m0.000s
+++ /dev/null
-scp main.pdf wking@einstein.physics.drexel.edu:./public_html/course/notes/ring_Efield.pdf
+++ /dev/null
-\documentclass[letterpaper, 10pt]{article}
-
-\usepackage{hyperref}
-\usepackage{fancyvrb}
-\usepackage{relsize}
-\usepackage{fullpage}
-
-% finish setting up hyperref
-\hypersetup{pdfauthor={W.\ Trevor King}}
-\hypersetup{pdfsubject={Cluster Tools}}
-\hypersetup{pdftitle={Batch Queue Job Control}}
-\hypersetup{pdfstartview=FitH} % zooming to fit the page width.
-\hypersetup{colorlinks} % don't do the ugly boxes around links
-
-\renewcommand{\maketitle}{%
- \begin{center}
- {\Large Cluster Tools} \\
- Batch Queue Job Control \\
- W.\ Trevor King \\
- \today
- \end{center}
-}
-
-\setlength{\parindent}{0pt}
-\setlength{\parskip}{0.5\baselineskip}
-
-\newcommand{\inputfilesimple}[1]{\VerbatimInput[fontsize=\relsize{-1}]{#1}}
-\newcommand{\inputfile}[2]{\VerbatimInput[fontsize=\relsize{-1},frame=single,label=#2]{#1}}
-
-\newcommand{\Con}{\DefineShortVerb{\|}} % code: |grep|
-\newcommand{\Coff}{\UndefineShortVerb{\|}}
-\newcommand{\mC}[1]{\emph{<#1>}} % meta-code: <regexp>
-\newcommand{\bs}{$\backslash$}
-
-% input the output of a shell command,
-% \com{<command>}{<file_basename>}
-% \com{echo hello world}{hello_world}
-\newcommand{\com}[2]{\inputfilesimple{#2_out}}
-% run a command silently (don't input the output)
-% \scom{sleep 10}
-\newcommand{\scom}[1]{}
-% run a queued command (single word arguments only)
-% \qcom{simple_echo.sh}
-\newcommand{\qcom}[1]{\inputfilesimple{#1_out}}
-\newcommand{\comout}{} % input the sdtout from the last queued command
-
-\newcommand{\home}{$\sim$} % print a tilde (user home directory shortcut)
-
-%-----------------------end preamble-------------------------
-
-\begin{document}
-\Con
-
-\maketitle
-
-\input{submitting}
-\input{querying}
-\input{altering}
-\input{example1}
-\input{utilities}
-
-\end{document}
+++ /dev/null
-#!/bin/bash
-#
-# run an example command and assemble its output for printing
-
-RunLoud ()
-{
- BASEFILE=$1
- shift
- echo "\$ $*" > ${BASEFILE}_out
- $* >> ${BASEFILE}_out 2> ${BASEFILE}_err
-}
-
-PREVQFILE=""
-cat command_list | while read COM
- do
- echo "$COM"
- if [ "${COM:0:6}" == "COMOUT" ] # print the stdout output of the last job
- then # note, you need to wait long enough for it to exist!
- # also note, it must be the most recent job stdout (\scom{sleep ...})
- echo " ... time passes ..." >> ${PREVQFILE}_out
- FILE=`/bin/ls -t *.o[0-9]* | head -n1`
- echo "\$ cat $FILE" >> ${PREVQFILE}_out
- cat $FILE >> ${PREVQFILE}_out
- elif [ "${COM:0:5}" == "QCOM " ] # run a queued job
- then
- COM="${COM:5}" # "QCOM bla bla bla" --> "bla bla bla"
- ./$COM > comO 2> comE
- > ${COM}_out
- # insert '# ' in front of lines without leading spaces (except 'done')
- # insert '> ' in front of lines with leading spaces
- sed 's/^\([^[:space:]].*\)/$ \1/;s/$ done/> done/;s/^\([[:space:]].*\)/> \1/' $COM > ${COM}_out
- cat comO >> ${COM}_out
- if [ ! -s comE ] # file has no size
- then
- rm -f comE
- else
- echo "errors! executing a job, see comE"
- echo -e "\non job: $COM" >> comE
- #exit 0
- fi
- rm -f comO
- PREVQFILE="$COM"
- sleep 1
- elif [ "${COM:0:4}" == "COM " ]
- then
- # run a non-silent shell command
- COM=${COM:4} # "COM outfile echo 'hi'" --> "outfile echo 'hi'"
- RunLoud $COM
- else
- # run a silent shell command
- $COM
- fi
-done
-
-echo "complete"
-
-exit 0
+++ /dev/null
-#!/bin/bash
-
-for FILE in $*
-do
- sed -n 's/.*\\com{\(.*\)}{\(.*\)}.*/COM \2 \1/p;s/.*\\scom{\(.*\)}.*/\1/p;s/.*\\qcom{\(.*\)}.*/QCOM \1/p;s/.*\\comout.*/COMOUT/p' $FILE
-done
+++ /dev/null
-Running a job...
+++ /dev/null
-Running a job...
+++ /dev/null
-echo "sleep 30 && echo 'Running a job...'" | qsub -N myjob
+++ /dev/null
-$ echo "sleep 30 && echo 'Running a job...'" | qsub -N myjob
-2707.n0.physics.drexel.edu
+++ /dev/null
-JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub -W depend=afterok:3`
-qstat && qalter -h n $JOBID && echo "hold removed" && qstat
+++ /dev/null
-$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub -W depend=afterok:3`
-$ qstat && qalter -h n $JOBID && echo "hold removed" && qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2725.n0 STDIN sysadmin 0 R batch
-2726.n0 STDIN sysadmin 0 R batch
-2727.n0 STDIN sysadmin 0 H batch
-hold removed
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2725.n0 STDIN sysadmin 0 R batch
-2726.n0 STDIN sysadmin 0 R batch
-2727.n0 STDIN sysadmin 0 Q batch
+++ /dev/null
-JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-qdel $JOBID
-echo "deleted $JOBID" && qstat
+++ /dev/null
-$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-$ qdel $JOBID
-$ echo "deleted $JOBID" && qstat
-deleted 2728.n0.physics.drexel.edu
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2725.n0 STDIN sysadmin 0 R batch
-2726.n0 STDIN sysadmin 0 R batch
-2727.n0 STDIN sysadmin 0 R batch
+++ /dev/null
-$ qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2722-1.n0 STDIN-1 sysadmin 0 R batch
-2722-2.n0 STDIN-2 sysadmin 0 R batch
-2722-3.n0 STDIN-3 sysadmin 0 R batch
-2722-4.n0 STDIN-4 sysadmin 0 R batch
-2722-5.n0 STDIN-5 sysadmin 0 R batch
-2723.n0 STDIN sysadmin 0 H batch
+++ /dev/null
-$ qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2721-1.n0 STDIN-1 sysadmin 0 R batch
-2721-2.n0 STDIN-2 sysadmin 0 R batch
-2721-3.n0 STDIN-3 sysadmin 0 R batch
-2721-4.n0 STDIN-4 sysadmin 0 R batch
-2721-5.n0 STDIN-5 sysadmin 0 R batch
+++ /dev/null
-$ qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2712.n0 STDIN sysadmin 0 R batch
-2713.n0 STDIN sysadmin 0 R batch
-2714.n0 STDIN sysadmin 0 H batch
+++ /dev/null
-JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-sleep 2 && qstat -f
+++ /dev/null
-$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-$ sleep 2 && qstat -f
-Job Id: 2725.n0.physics.drexel.edu
- Job_Name = STDIN
- Job_Owner = sysadmin@n0.physics.drexel.edu
- job_state = R
- queue = batch
- server = n0.physics.drexel.edu
- Checkpoint = u
- ctime = Thu Jun 26 13:58:54 2008
- Error_Path = n0.physics.drexel.edu:/home/sysadmin/howto/cluster/pbs_queues
- /STDIN.e2725
- exec_host = n8/0
- Hold_Types = n
- Join_Path = n
- Keep_Files = n
- Mail_Points = a
- mtime = Thu Jun 26 13:58:55 2008
- Output_Path = n0.physics.drexel.edu:/home/sysadmin/howto/cluster/pbs_queue
- s/STDIN.o2725
- Priority = 0
- qtime = Thu Jun 26 13:58:54 2008
- Rerunable = True
- Resource_List.nodect = 1
- Resource_List.nodes = 1
- Resource_List.walltime = 01:00:00
- session_id = 18020
- Variable_List = PBS_O_HOME=/home/sysadmin,PBS_O_LANG=en_US.UTF-8,
- PBS_O_LOGNAME=sysadmin,
- PBS_O_PATH=/home/sysadmin/bin:/usr/local/bin:/usr/local/sbin:/usr/bin
- :/usr/sbin:/bin:/sbin:/usr/X11R6/bin:/usr/local/maui/bin:/home/sysadmi
- n/script:/home/sysadmin/bin:.,PBS_O_MAIL=/var/mail/sysadmin,
- PBS_O_SHELL=/bin/bash,PBS_SERVER=n0.physics.drexel.edu,
- PBS_O_HOST=n0.physics.drexel.edu,
- PBS_O_WORKDIR=/home/sysadmin/howto/cluster/pbs_queues,
- PBS_O_QUEUE=batch
- etime = Thu Jun 26 13:58:54 2008
- start_time = Thu Jun 26 13:58:55 2008
- start_count = 1
-
+++ /dev/null
-$ qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2707.n0 myjob sysadmin 0 Q batch
+++ /dev/null
-JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-sleep 2 && qstat $JOBID
+++ /dev/null
-$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-$ sleep 2 && qstat $JOBID
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2724.n0 STDIN sysadmin 0 R batch
+++ /dev/null
-$ qstat -q
-
-server: n0
-
-Queue Memory CPU Time Walltime Node Run Que Lm State
----------------- ------ -------- -------- ---- --- --- -- -----
-batch -- -- -- -- 2 0 -- E R
- ----- -----
- 2 0
+++ /dev/null
-$ qstat -B
-Server Max Tot Que Run Hld Wat Trn Ext Status
----------------- --- --- --- --- --- --- --- --- ----------
-n0.physics.drexe 0 2 0 2 0 0 0 0 Active
+++ /dev/null
-qstat: Unknown queue destination |
-qstat: Unknown queue destination grep
-qstat: Unknown queue destination '[.]walltime'
+++ /dev/null
-$ qstat -f | grep '[.]walltime'
+++ /dev/null
-$ qstat
-Job id Name User Time Use S Queue
-------------------------- ---------------- --------------- -------- - -----
-2705.n0 STDIN sysadmin 0 Q batch
+++ /dev/null
-\section{Querying}
-\label{sec.qstat}
-
-You can get information about currently running and queued jobs with |qstat|.
-In the examples in the other sections, we've been using bare |qstat|s to get information about the status of jobs in the queue.
-You get information about a particular command with
-\qcom{qstat_particular_echo.sh}
-and you can get detailed information on a every command (or a particular one, see previous example) with the |-f| (full) option.
-\scom{sleep 40}
-\qcom{qstat_full_echo.sh}
-
-The |qstat| command gives you lots of information about the current state of a job, but to get a history you should use the |tracejob| command.
-\qcom{tracejob_echo.sh}
-
-
-You can also get the status of the queue itself by passing |-q| option to |qstat|
-\com{qstat -q}{qstat_queue_info}
-or the status of the server with the |-B| option.
-\com{qstat -B}{qstat_server_info}
-
-You can get information on the status of the various nodes with |qnodes| (a symlink to |pbsnodes|).
-The output of |qnodes| is bulky and not of public interest, so we will not reproduce it here.
-For more details on flags you can pass to |qnodes|/|pbsnodes| see |man pbsnodes|,
-but I haven't had any need for fancyness yet.
+++ /dev/null
-#!/bin/bash
-#
-# run_vel_dist.sh
-#
-# run N simulations each at a series of pulling speeds V
-# (non-velocity parameters are copied from the get_vel_dist.sh command line)
-# for each speed, save all unfolding data data_$V, and
-# generate a histogram of unfolding forces hist_$V
-# also generate a file v_dep with the mean unfolding force vs velocity
-
-# We can't depend on the entire array in one shot, so
-# batch executions into a single array instance
-BN=100 # sawsim executions per array job instance
-N=50 # instances in a single array
-Vs=".2e-6 .5e-6 1e-6 2e-6 5e-6"
-SAFTEY_SLEEP=2 # seconds to sleep between spawning array job and depending on it
- # otherwise dependencies don't catch
-
-STAMP=`date +"%Y.%m.%d.%H.%M.%S"`
-mkdir v_dep-$STAMP || exit 1
-cd v_dep-$STAMP
-echo "Date "`date` > v_dep_notes
-echo "Run$ sawsim $* -v \$V" >> v_dep_notes
-echo "for V in $*" >> v_dep_notes
-
-Is="" # build a list of allowed 'i's, since 'for' more compact than 'while'
-i=1
-while [ $i -le $N ]
- do
- Is="$Is $i"
- let "i += 1"
-done
-
-vdone_condition="afterany"
-VJOBIDS=""
-for V in $Vs
-do
- # run N sawtooth simulations
- idone_condition="afterany"
- cmd="cd \$PBS_O_WORKDIR
- i=1
- while [ \$i -le $BN ]; do
- ~/sawsim/sawsim $* -v $V > run_$V-\$PBS_ARRAYID-\$i
- let \"i += 1\"
- done"
- JOBID=`echo "$cmd" | qsub -h -t 1-$N -N "sawsim" -o run_$V.o -e run_$V.e` || exit 1
- # "3643.abax.physics.drexel.edu" --> "3643"
- ARRAYID=`echo "$JOBID" | sed "s/\\([0-9]*\\)\\([.].*\\)/\\1/g"`
- for i in $Is; do idone_condition="$idone_condition:$ARRAYID-$i"; done
-
- sleep $SAFTEY_SLEEP
- # once they're done, compile a list of all unfolding forces for each speed
- JOBID=`echo "cd \\\$PBS_O_WORKDIR && cat run_$V-* | grep -v '#' > data_$V" |\
- qsub -h -W depend="$idone_condition" -N sawComp -o data_$V.o -e data_$V.e` \
- || exit 1
- vdone_condition="$vdone_condition:$JOBID"
- VJOBIDS="$VJOBIDS $JOBID"
- for i in $Is; do qrls "$ARRAYID-$i"; done
-done
-# once we have force lists for each velocity, make histograms and F(V) chart
-echo "Final job :"
-echo "cd \$PBS_O_WORKDIR && ../vel_dist_graph.sh $Vs" | \
- qsub -W depend="$vdone_condition" -N sawsimGraph || exit 1
-for job in $VJOBIDS; do qrls $job; done
-cd ..
-
-exit 0
+++ /dev/null
-echo "sleep 30 && echo 'Running a job...'" | qsub -l walltime=15:00
+++ /dev/null
-$ echo "sleep 30 && echo 'Running a job...'" | qsub -l walltime=15:00
-2711.n0.physics.drexel.edu
+++ /dev/null
-echo "sleep 30 && echo 'Running a job...'" | qsub
+++ /dev/null
-$ echo "sleep 30 && echo 'Running a job...'" | qsub
-2705.n0.physics.drexel.edu
+++ /dev/null
-qsub echo_script.sh
+++ /dev/null
-$ qsub echo_script.sh
-2706.n0.physics.drexel.edu
+++ /dev/null
-\section{Submitting jobs}
-\label{sec.qsub}
-
-You can submit jobs to the batch queue for later proccessing with |qsub|.
-Batch queueing can get pretty fancy, so |qsub| comes with lots of options (see |man qsub|).
-For the most part, you can trust your sysadmin to have set up some good defaults, and not worry about setting any options explicitly.
-As you get used to the batch queue system, you'll want tighter control of how your jobs execute by invoking more sophisticated options yourself, but don't let that scare you off at the beginning.
-They are, after all, only \emph{options}.
-This paper will give you a good start on the options I find myself using most often.
-
-\subsection{Simple submission}
-
-The simplest example of a job submission is:
-\qcom{simple_echo.sh}
-Which submits a job executing |sleep 30 \&\& echo 'Running a job...'| to the queue.
-The job gets an identifying ID in the queue, which |qsub| prints to |stdout|.
-
-You can check the status of your job in the queue with |qstat|.
-\com{qstat}{qstat_simple_echo}
-There is more information on |qstat| in Section \ref{sec.qstat}.
-
-If your job is too complicated to fit on a single line, you can save it in a sctipt and submit the script.
-\inputfile{echo_script.sh}{echo\_script.sh}
-\qcom{simple_script.sh}
-All the arguments discussed in later sections for the command line should have comment-style analogs that you can enter in your script if you use the script-submission approach with |qsub|.
-
-Note that you \emph{cannot} run executibles (non-shell-scripts) directly with |qsub|.
-For example
-\begin{Verbatim}
-$ cat script.py
-#!/usr/bin/python
-print "hello world!"
-$ qsub python script.py
-\end{Verbatim}
-% $ (close math-mode highlighting in emacs)
-will fail because |python| is an executible.
-Either use
-\begin{Verbatim}
-$ echo python script.py | qsub
-\end{Verbatim}
-% $ (close math-mode highlighting in emacs)
-wrap your |python| script in a |bash| script
-\begin{Verbatim}
-$ cat wrapper.sh
-#!/bin/bash
-python script.py
-$ qsub wrapper.sh
-\end{Verbatim}
-or run your |python| script directly
-\begin{Verbatim}
-$ qsub script.py
-\end{Verbatim}
-
-
-\subsection{IO: Job names and working directories}
-
-You will often be interested in the |stdout| and |stderr| output from your jobs.
-The batch queue system saves this information for you (to the directory from which you called |qsub|)
-in two files \mC{jobname}|.o|\mC{jobID-number} and \mC{jobname}|.e|\mC{jobID-number}.
-Job IDs we have seen before, they're just the numeric part of |qsub| output (or the first field in the |qstat| output).
-Job IDs are assigned by the batch queue server, and are unique to each job.
-Job names are assigned by the job submitter (that's you) and need not be unique.
-They give you a method for keeping track of what job is doing what task, since you have no control over the job ID.
-The combined \mC{jobname}|.|\mC{jobID-number} pair is both unique (for the server) and recognizable (for the user), which is why it's used to label the output data from a given job.
-You control the job name by passing the |-n |\mC{jobname} argument to |qsub|.
-\scom{sleep 40}
-\qcom{named_echo.sh}
-\com{qstat}{qstat_named_echo}
-
-Perhaps you are fine with |stdin| and |stdout|, but the default naming scheme, even with the job name flexibility, is too restrictive.
-No worries, |qsub| lets you specify exactly which files you'd like to use with the unsurprisingly named |-o| and |-e| options.
-\qcom{explicit_oe_echo.sh}
-\scom{sleep 2}
-\com{cat my_out}{explicit_oe_echo_o}
-\com{cat my_err}{explicit_oe_echo_e}
-
-A time will come when you are no longer satified with |stdin| and |stdout| and you want to open your own files or worse, run a program!
-Because no sane person uses absolute paths all the time, we need to know what directory we're in so we can construct our relative paths.
-You might expect that your job will execute from the same directory that you called qsub from, but that is not the case.
-I think the reason is that that directory is not garaunteed to exist on the host that eventually runs your program.
-In any case, your job will begin executing in your home directory.
-Writing relative paths from your home directory is about as annoying as writing absolute paths, so |qsub| gives your script a nifty environment variable |PBS\_O\_WORKDIR|, which is set to the directory you called |qsub| from.
-Since \emph{you} know that this directory exists on the hosts (since the home directories are NFS mounted on all of our cluster nodes), you can move to that directory yourself, using something like
-\scom{sleep 40}
-\qcom{workdir_echo.sh}
-\scom{sleep 2}
-\comout
-Note that if we had enclosed the echo argument in double quotes (|\"|), we would have to escape the `|\$|' symbol in our |echo| argument so that it survives the shell expansion and makes it safely into |qsub|'s input.
-
-
-\subsection{Long jobs}
-
-If you have jobs that may take longer than the default wall time (currently 1 hour), you will need to tell the job manager.
-Walltimes may seem annoying, since you don't really know how long a job will run for,
-but they protect the cluster from people running broken programs that waste nodes looping around forever without accomplishing anything.
-Therefor, your walltime doesn't have to be exactly, or even close to, your actual job execution time.
-Before submitting millions of long jobs, it is a good idea to submit a timing job to see how long your jobs should run for.
-Then set the walltime a factor of 10 or so higher.
-For example
-\qcom{get_walltime_echo.sh}
-\scom{sleep 40}
-\comout
-\qcom{set_walltime_echo.sh}
-\scom{sleep 2}
-\com{qstat -f | grep '[.]walltime'}{qstat_set_walltime_echo}
-\scom{sleep 38}
-You can set walltimes in |[[H:]M:]S| format, where the number of hours, minutes, and seconds are positive integers.
-I passed the |-j oe| combines both |sdtout| and |stdin| streams on |stdin| because |time| prints to |stderr|.
-Walltimes are only accurate on the order of minutes and above, but you probably shouldn't be batch queueing jobs that take so little time anyway.
-
-\subsection{Job dependencies}
-
-You will often find yourself in a situation where the execution of one job depends on the output of another job.
-For example, |jobA| and |jobB| generate some data, and |jobC| performs some analysis on that data.
-It wouldn't do for |jobC| to go firing off as soon as there was a free node, if there was no data available yet to analyze.
-We can deal with \emph{dependencies} like these by passing a |-W depend=|\mC{dependency-list} option to |qsub|.
-The dependency list can get pretty fancy (see |man qsub|), but for the case outlined above, we'll only need |afterany| dependencies (because |jobC| should execute after jobs |A| and |B|).
-
-Looking at the |man| page, the proper format for our dependency list is |afterany:jobid[:jobid...]|, so we need to catch the job IDs output by |qsub|.
-We'll just use the |bash| ``back tick'' command substitution operators (|`|) for this.
-\qcom{depend_echo.sh}
-\scom{sleep 2}
-\com{qstat}{qstat_depend_echo}
-\scom{sleep 50}
-\com{cat C_out}{depend_echo_out}
-Note that we have to escape the |PBS\_O\_WORKDIR| expansion twice.
-The back tick expansion expands
- |\bs\bs\bs\$PBS\ldots| to
- |\bs\$PBS\ldots|.
-The double quote expansion when evaluating the echo command expands that to
- |\$PBS\ldots|.
-When the job finally runs, we actually expand out to our working directory.
-
-
-\subsection{Job arrays}
-
-If you have \emph{lots} of jobs you'd like to submit at once, it is tempting try
-\qcom{while_echo.sh}
-This does work, but it puts quite a load on the server as the number of jobs gets large.
-In order to allow the execution of such repeated commands the batch server provides \emph{job arrays}.
-You simply pass |qsub| the |-t array\_request| option, listing the range or list of IDs for which you'd like to run your command.
-\scom{sleep 10}
-\qcom{array_echo.sh}
-\scom{sleep 2}
-\com{qstat}{qstat_array_echo}
-
-One possibly tricky issue is depending on a job array.
-If you have an analysis job that you need to run to compile the results of your whole array, try
-\scom{sleep 50}
-\qcom{array_depend_echo.sh}
-\scom{sleep 2}
-\com{qstat}{qstat_array_depend_echo}
-\scom{sleep 60}
-\com{cat sum_out}{array_depend_echo_out}
-Note that you must create any files needed by the dependent jobs \emph{during} the early jobs.
-The dependent job may start as soon as the early jobs finish, \emph{before} the |stdin| and |stdout| files for some early jobs have been written.
-Sadly, depending on either the returned job ID or just its numeric portion doesn't seem to work.
-
-It is important that the jobs on which you depend are loaded into the server \emph{before your depending job is submitted}.
-To ensure this, you may need to add a reasonable sleep time between submitting your job array and submitting your dependency.
-However, your depending job will also hang if some early jobs have \emph{already finished} by the time you get around to submitting it.
-
-Despite the annoyance, a single sleep per job array is cheaper than a sleep after each non-array job submission to avoid crashing the server in the |while|-loop approach.
-See the examples sections and |man qsub| for more details.
+++ /dev/null
-JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-sleep 2 && tracejob $JOBID
+++ /dev/null
-$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
-$ sleep 2 && tracejob $JOBID
-
-Job: 2726.n0.physics.drexel.edu
-
-06/26/2008 13:58:57 S enqueuing into batch, state 1 hop 1
-06/26/2008 13:58:57 S Job Queued at request of sysadmin@n0.physics.drexel.edu, owner = sysadmin@n0.physics.drexel.edu, job name = STDIN, queue = batch
-06/26/2008 13:58:58 S Job Modified at request of root@n0.physics.drexel.edu
-06/26/2008 13:58:58 S Job Run at request of root@n0.physics.drexel.edu
-06/26/2008 13:58:58 S Job Modified at request of root@n0.physics.drexel.edu
+++ /dev/null
-\section{Utilities}
-\label{sec.utilities}
-
-After playing around on the cluster for a while, I've developed some utilities to integrate job submission with the rest of my workflow.
-So far, I have written
- |dup\_env| for setting up an environment like the one you called qsub from,
- |qcmd| for submitting a single command as a job,
- and
- |qcmds| for submitting lots of one-line jobs and waiting until they complete.
-
-\subsection{dup\_env}
-
-When |qsub| starts your job on a compute node, it sets up your environmental variables for you.
-Unfortunately, it doesn't do this by cloning your old environment, for example your new |PATH| will come from |/etc/bash.bashrc| (I think?).
-Your old |PATH| get's stored in |PBS\_O\_PATH| (see |man qsub|).
-|dup\_env| just loops through your current environment and overrides |qsub|'s decisions and reinstalls your original enviroment.
-There may be, of course, some exceptions, since you don't want to set your |HOST| to the host you called |qsub| from.
-Remember to place |dup\_env| somewhere where your restricted |qsub| path will find it.
-\inputfile{file/dup_env}{\home/bin/dup\_env}
-
-\subsection{qcmd}
-
-I often have scripts with a few big, slow jobs at the beginning, generating some data that I process in the remainder of the script.
-Rather than chew up the processors on the master node, I'd rather bump them out to the compute nodes.
-To make this alteration as painless as possible, I've written |qcmd| which submits the command in your current environment, waits for the job to finish, and outputs the job's |stdout|/|stderr|/exit-status as it's own.
-You can carry on exactly as if the job executed on your local machine.
-The script works by listening at your mailbox for the job completion email from the queue manager, but I talk about all that in the script itself.
-\inputfile{file/qcmd}{\home/script/qcmd}
-
-\subsection{qcmds}
-
-With three processes open for each waiting job, |qcmd| scales pretty poorly.
-For scripts where you need a bit more muscle to handle several tens to thousands of jobs, I wrote |qcmds|.
-|qcmds| is almost identical to |qcmd|, except that where you had one |qcmd| instance per job, now you have one |qcmds| instance per \emph{set} of jobs.
-With a whole bunch of jobs and only one |stdout|, |qcmds| needed a seperate interface.
-You just pipe your endline (`|\bs n|') delimited jobs into |qcmds| |stdin|, and out the |stdout| comes a list of completing jobs, in a tab delimited list for easy processing.
-Run the examples suggested in the script comments to get a feel for how these work.
-\inputfile{file/qcmds}{\home/script/qcmds}
-
-\subsection{qcleanmail}
-
-Both |qcmd| and |qcmds| listen for job-completion emails from the queue manager, and these can fill up your inbox pretty quickly.
-I wrote this little script to run through my mailboxes and delete all PBS-related messages.
-\inputfile{file/qcleanmail}{\home/script/qcleanmail}
-
-The referenced |procmail| filter is:
-\inputfile{file/qcleanmail.proc}{\home/.mailspool/mailfilter/qcleanmail.proc}
-
-In order to avoid filling up my system mailox with PBS junk between calls to |qcleanmail|, I use the following |\$HOME/.procmailrc| filter to deflect PBS messages to |\$HOME/.mailspool/completed|:
-\inputfile{file/_procmailrc}{\home/.procmailrc}
+++ /dev/null
-i=0
-while [ $i -le 5 ]
- do
- JOBID=`echo "echo 'Running a job...'" | qsub`
- let "i += 1"
-done
+++ /dev/null
-$ i=0
-$ while [ $i -le 5 ]
-> do
-> JOBID=`echo "echo 'Running a job...'" | qsub`
-> let "i += 1"
-> done
+++ /dev/null
-echo 'pwd && cd $PBS_O_WORKDIR && pwd' | qsub
+++ /dev/null
-$ echo 'pwd && cd $PBS_O_WORKDIR && pwd' | qsub
-2709.n0.physics.drexel.edu
- ... time passes ...
-$ cat STDIN.o2709
-/home/sysadmin
-/home/sysadmin/howto/cluster/pbs_queues
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